Variant chr2-227329765-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001277067.1(MFF):c.-54G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 1,538,830 control chromosomes in the GnomAD database, including 94,120 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.29 ( 6853 hom., cov: 32)

Exomes 𝑓: 0.36 ( 87267 hom. )

Consequence

MFF
NM_001277067.1 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.15

Variant links:

Genes affected

MFF (HGNC:24858): (mitochondrial fission factor) This is a nuclear gene encoding a protein that functions in mitochondrial and peroxisomal fission. The encoded protein recruits dynamin-1-like protein (DNM1L) to mitochondria. There are multiple pseudogenes for this gene on chromosomes 1, 5, and X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]

MFF links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0019381642).

BP6

Variant 2-227329765-G-T is Benign according to our data. Variant chr2-227329765-G-T is described in ClinVar as [Benign]. Clinvar id is 379994.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MFF	NM_001277062.2 link	c.-40-861G>T		intron_variant	Intron 2 of 8	ENST00000304593.14	NP_001263991.1	Q9GZY8-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MFF	ENST00000304593.14 link	c.-40-861G>T		intron_variant	Intron 2 of 8	2	NM_001277062.2	ENSP00000304898.10		Q9GZY8-2

Frequencies

GnomAD3 genomes

AF:

0.288

AC:

43631

AN:

151312

Hom.:

6857

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.250

Gnomad ASJ

AF:

0.388

Gnomad EAS

AF:

0.234

Gnomad SAS

AF:

0.466

Gnomad FIN

AF:

0.302

Gnomad MID

AF:

0.353

Gnomad NFE

AF:

0.376

Gnomad OTH

AF:

0.290

GnomAD3 exomes

AF:

0.321

AC:

79076

AN:

246018

Hom.:

12677

AF XY:

0.337

AC XY:

44803

AN XY:

132976

show subpopulations

Gnomad AFR exome

AF:

0.121

Gnomad AMR exome

AF:

0.199

Gnomad ASJ exome

AF:

0.375

Gnomad EAS exome

AF:

0.225

Gnomad SAS exome

AF:

0.449

Gnomad FIN exome

AF:

0.299

Gnomad NFE exome

AF:

0.368

Gnomad OTH exome

AF:

0.334

GnomAD4 exome

AF:

0.356

AC:

494532

AN:

1387398

Hom.:

87267

Cov.:

AF XY:

0.361

AC XY:

250084

AN XY:

692718

show subpopulations

Gnomad4 AFR exome

AF:

0.121

Gnomad4 AMR exome

AF:

0.205

Gnomad4 ASJ exome

AF:

0.379

Gnomad4 EAS exome

AF:

0.249

Gnomad4 SAS exome

AF:

0.449

Gnomad4 FIN exome

AF:

0.305

Gnomad4 NFE exome

AF:

0.370

Gnomad4 OTH exome

AF:

0.338

GnomAD4 genome

AF:

0.288

AC:

43621

AN:

151432

Hom.:

6853

Cov.:

AF XY:

0.285

AC XY:

21055

AN XY:

73914

show subpopulations

Gnomad4 AFR

AF:

0.132

Gnomad4 AMR

AF:

0.250

Gnomad4 ASJ

AF:

0.388

Gnomad4 EAS

AF:

0.234

Gnomad4 SAS

AF:

0.464

Gnomad4 FIN

AF:

0.302

Gnomad4 NFE

AF:

0.376

Gnomad4 OTH

AF:

0.286

Alfa

AF:

0.364

Hom.:

26284

TwinsUK

AF:

0.396

AC:

1469

ALSPAC

AF:

0.383

AC:

1476

ESP6500AA

AF:

0.117

AC:

516

ESP6500EA

AF:

0.347

AC:

2985

ExAC

AF:

0.330

AC:

40028

Asia WGS

AF:

0.297

AC:

1035

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Dec 02, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.35

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.035

T;T;.

Eigen

Benign

-0.28

Eigen_PC

Benign

-0.11

FATHMM_MKL

Uncertain

0.82

LIST_S2

Benign

0.65

T;T;T

MetaRNN

Benign

0.0019

T;T;T

MetaSVM

Benign

-0.96

MutationAssessor

Benign

1.4

L;.;.

PrimateAI

Benign

0.37

PROVEAN

Benign

-0.43

N;D;N

REVEL

Benign

0.033

Sift

Benign

0.065

T;.;T

Sift4G

Benign

0.15

T;T;T

Polyphen

0.079

B;.;.

Vest4

0.062

MPC

0.32

ClinPred

0.011

GERP RS

3.1

Varity_R

0.083

gMVP

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over